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Macbook Pro (M1 2020) Set-up

MacBook Pro M1 (2020) Set-Up 👩‍💻

This is Steph's "living" document with instructions/documentation of my set-up on a MacBook Pro M1 (2020), with a focus on #rstats data science and meta tools 📊

Point & Click Software 🖱

Software Set Up & Tweaks 🍽

MacBook 💻

Safari 🦒

  • Safari > Preferences > Advanced > Show full website address
  • Safari > Preferences > Advanced > Show Develop menu
  • Safari > View > Show status bar

Finder 🔎

  • Show dotfiles
    • one time: Cmd + Shift + .
    • to show them all the time: (from Terminal) defaults write com.apple.finder AppleShowAllFiles -bool YES; killall Finder
    • to hide them again: (from Terminal) defaults write com.apple.finder AppleShowAllFiles -bool NO; killall Finder

Alfred 🕵️

Demo and how to tailor the App in this YouTube video. "Register" the .Rproj file-type with Alfred:

  • Go to Alfred’s Preferences > Features > Default Results > Advanced
  • Drag any .Rproj file onto this space and then close

Homebrew 🧃

Installed homebrew on a Macbook with M1/Apple Chip https://stackoverflow.com/questions/66666134/how-to-install-homebrew-on-m1-mac, and then immediately implemented this fix when homebrew bonked installing Git 😳 Homebrew/discussions#501

The biggest M1 difference seems to be setting the PATH to homebrew manually in your Terminal dot file, so putting export PATH=/opt/homebrew/bin:$PATH in ~.zshrc.

R & RStudio 🇷

R Library

cd && mkdir Rlibrary
echo R_LIBS=~/Rlibrary >> .Renviron

RStudio Global Defaults

RStudio >> Tools >> Global Options >> General >> Basic:

  • untick Restore .RData into workspace at startup
  • Save workspace to .RData on exit: <NEVER>

RStudio >> Tools >> Global Options >> General >> Advanced:

  • tick Show .Last.value in environment listing

RStudio Terminal

RStudio >> Tools >> Global Options >> Terminal

  • new terminals open with:

R/RStudio & Homebrew

If R or RStudio are opened via the Terminal then the PATH to homebrew will be accessed via the ~.zshrc file. However, not if opened using the Dock. Add PATH="/opt/homebrew/bin:${PATH}" to your ~.Renviron file if you need R/RStudio to access homebrew.

LaTeX

Using LaTeX` distribution from {tinytex} which is built especially for using with R.

In R:

install.packages("tinytex")
tinytex::install_tinytex()

I had to implement this fix in the Terminal (to gain write access to /usr/local/bin) to install {tinytex} rstudio/tinytex#24.

I also had to implement this fix to get extrafont::font_import() to work wch/extrafont#88

remove.packages("Rttf2pt1")
remotes::install_version("Rttf2pt1", version = "1.3.8")

Git & GitHub 🗂️

Git: Install and Configure Git

brew install git
git config --global user.email firstname.lastname@gov.bc.ca
git config --global user.name "Firstname Lastname"
git config --global core.editor "nano"
git config --global credential.helper osxkeychain

GitHub: Set Up GitHub Authorization

install.packages("gitcreds")
library(gitcreds)
gitcreds_set()

First Git Push/Pull

Set default for Pull, I use the previous Git default (see SO issue with warning message & discussion/options)

git config pull.rebase false

I "vaccinated" my global gitignore with {usethis}'s git_vaccinate(), details here https://usethis.r-lib.org/reference/git_vaccinate.html

Some System Libraries for R Packages ⚙️

Xquartz

Xquartz is a graphics device for R

brew install xquartz

qpdf

Split, Combine and Compress PDF files using the {qpdf} R package, installing the C++ source library:

brew install qpdf

Magick & Friends

To build packages from source (i.e., new releases or development versions from GitHub):

brew install libsvg curl libxml2 boost

## imagemagick for command-line image manipulation and use of the 'magick' R package
brew install imagemagick

Mapshaper

## `rmapshaper` R package has a size limit

brew install node
npm install -g mapshaper

VS Code

Install Visual Studio Code and add in Extensions:

  • GitHub Pull Requests & Issues
  • Jupyter
  • Python, Pylance
  • R, R debugger
  • Markdown All in One
  • Path Autocomplete

Install R packages languageserver and httpgd and radian from Terminal pip3 install -U radian

Use Shift-Command-P in VSCode to Open Settings (setting.json) and/ or Keyboard Shortcuts (keybindings.json) to edit and personalize.

Python & JupyterLab

I use the Miniforge installation for arm64/Apple Silicon/M1. I downloaded the sh file, ran bash filename.sh in the Terminal and followed the prompts. I then used the UBC MDS Software stack install instructions for macOS for adding some Python packages using conda install.

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